Methods to control gene expression by silencing or suppressing a target gene include use of antisense, co-suppression, and RNA interference. Anti-sense gene suppression in plants is described by Shewmaker et al. in U.S. Pat. Nos. 5,107,065, 5453,566, and 5,759,829. Gene suppression in bacteria using DNA which is complementary to mRNA encoding the gene to be suppressed is disclosed by Inouye et al. in U.S. Pat. Nos. 5,190,931, 5,208,149, and 5,272,065. RNA interference or double-stranded RNA-mediated gene suppression has been described by, e.g., Redenbaugh et al. in “Safety Assessment of Genetically Engineered Fruits and Vegetables”, CRC Press, 1992; Chuang et al. (2000) PNAS, 97:4985-4990; and Wesley et al. (2001) Plant J., 27:581-590.
In some cases, total or maximal silencing or suppression is desired, for example, where a suppression element is designed to suppress a pathogen target gene in order to achieve maximal protection of the host of that pathogen. However, complete suppression of a gene is not always preferred, for example, where complete suppression decreases viability or robustness of the organism in which the gene is silenced. In some cases, a desired phenotype (e.g., a particular level of a metabolite or a particular combination of traits) is associated with a specific level of suppression of a target gene. Thus, it is useful to be able to modify the level of silencing of a target gene or genes by a suppression element.